Course overview

    The H3Africa initiative is aimed at studying the genomic and environmental determinants of disease in Africa. The goals of H3Africa are to enhance the necessary genomic expertise among African scientists and to encourage collaborations between African investigators by supporting infrastructure development and research projects. The H3ABioNet aims to create a sustainable African Bioinformatics Network to support H3Africa researchers through the development of bioinformatics capacity on the continent. To achieve this vision the H3ABioNet will be hosting the first specialized bioinformatics training course for bioinformaticians and researchers within the network.

    The course is aimed at developing a core set of specialised skills amongst members in the network who are in a position to train others at their institutions. The course will train members who are required to efficiently manage and analyse the vast amount of genomic data generated by the various H3Africa projects.

    The course will be run over 3 weeks (6 days a week) and will cover both theoretical and practical aspects of a range of topics centered on the analysis of genomic and population-based data. An emphasis will be placed on allowing participants to develop hands-on experience with analysing real data using open source software, tools and resources.

    The course is open to all members within the H3A Bioinformatics Network, who have long term positions at one of the partner institutions and the capacity to train others in their institution when they return from the course.

    Course objectives

    The course is composed of a range of topics aimed at providing participants with the necessary hands-on practical skills to be able to manage and analyse genomic data. As well as specialized topics in population genetics, GWAS and next-generation sequence analysis, the course will include programming to ensure participants gain basic skills in data manipulation and management, and biostatistics to prepare them for statistical analysis of data.

    Course outline

    Programming using python – basic introduction through to advanced topics for managing and manipulating biological data. Will be run for 2 hours every morning for the duration of the course.

    Introduction to Linux – basic history and introduction through to complex commands for manipulating data and Bash scripting

    Data management – building simple MySQL queries and introduction to BioMart

    Biostatistics – basic probability theory, introduction to R, statistical hypothesis testing, principal component analysis, building regression models and visualisation

    Population genetics – content to be confirmed

    Genome-wide association studies – content to be confirmed

    Next-generation sequencing – introduction and QC, assembly and reference genome alignment, variant calling, RNA-seq data analysis, ChIP-seq data analysis, genome visualisation

    Course prerequisites

    Each course component will have prerequisites that participants will be required to complete or fulfill before the course starts. Participants will be notified of these requirements before the course commences.

    How to apply

    To apply to attend the course please complete the application form found here:

    http://surveys.h3abionet.org/icipe

    The deadline for applications is the 17th May 2013.

    Please ensure that all required information is completed on the application and that a motivation letter from your PI is attached.

    For those who are unable to attend the course in person, there will be the possible option of joining the course via live streaming to Tunis (Institut Pasteur) and IBADAN (NABDA-Southwest Center, University of Ibadan).

    Training Materials Availability:

    Training materials for this course are not currently available.


    Workshop training materials are available at: http://training.h3abionet.org/technical_workshop_2013/

    The H3Africa initiative is aimed at studying the genomic and environmental determinants of disease in Africa. The goals of H3Africa are to enhance the necessary genomic expertise among African scientists and to encourage collaborations between African investigators by supporting infrastructure development and research projects. H3ABioNet aims to create a sustainable African Bioinformatics Network to support H3Africa researchers through the development of bioinformatics capacity on the continent.

    In order to prepare for the large amount of data that will be generated by the various projects, the initial requirement is to set up the required computational infrastructure and resources to store, manage the data. To address this requirement, the H3ABioNet will be hosting a technical training course for H3ABioNet-funded staff and students.

    Course objectives

    The objective of the two-week training course is to equip H3ABioNet technical staff and students at the partner sites with the skills required to set up and maintain the necessary computational infrastructure and resources. The course will be both theoretical and practical, with an emphasis placed on hands-on experience in setting up and maintaining these resources. The course is aimed at individuals with a computational science background.

    Course outline

    Linux installation and system administration

    Galaxy installation, configuration and optimisation

    High performance computing, optimisation for genomic applications

    Security and data stewardship, firewalls, intrusion detection, data backups and archives, encryption, data privacy

    Data management, GridFTP, Globus Online, database design, web interfaces

    Genome databases, CHADO and BioMart,

    Data Visualisation, genome browsers, trackster and DAS

    Cloud computing, basic concepts, cloud services, creating virtual machines, deploying software environments, CloudMan, genome browsers

    Course prerequisites

    The course will have prerequisites that participants will be required to complete or fulfill before the course starts. Participants will be notified of these requirements before the course commences. The minimum requirement is a computer science/IT background with some Unix and programming experience.

    How to apply

    To apply to attend the course please complete the application form found here:

    http://surveys.h3abionet.org/sysadmincourse

    Please ensure that all required information is completed on the application and that a motivation letter from your PI is attached. The deadline for applications is the 10th May 2013


    The H3ABioNet recently co-organised a Scientific Communication Workshop from the 26th to the 27th of April 2021.
     
    The links below are the video recordings and resources that were used for the two days.
     

    Day 1 of Workshop: https://youtu.be/U2el7Zcyb-Y

    Day 2 of Workshop: https://youtu.be/XT8Lx8lR6-0

     

    Resources:

     
    1. Writing an effective abstract: Abstract document
    2. Communicating science exercise: Exercise document
    3. How to write good research manuscript: Manuscript document
    4. From trainee to tenure-track: Ten tips document
    5. How to give a “good” oral presentation: Oral presentation guidelines
    6. How to read, summarize, and critique a research article: Article critique document
    7. Opportunities for After Your Studies: Identifying Transferable Skills
    8. Personal Development Transferable Skills Profile and Action Plan: Transferable Skills Profile
    9. Transferable skills for a competitive edge: Transferable skills document

    Subcategories

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